I think this problem is not really related to
• Using the 2D dock instead of the 3D dock
• Using an older version of Adobe Flash
• Some other voodoo that might appear to work
as I've tried various combinations, and none of them really helped in the long run.
These are all just measures to decrease the load of the X3100 graphics chip. They might work temporarily, but when you try out a graphics intensive application (I don't know what kind of intensive, using a lot of memory or GPU instructions), or work with your MacBook for a long time without sending it to sleep, the problems reoccur.
There are two realistic scenarios, in my opinion:
1. Apple somehow managed to kill the X3100 drivers in Snow Leopard.
2. Our GPUs are all turning into toast over time, and it's just a coincidence we're all witnessing this problem right now. It might be some issue of flexing or overheating. When I push my CPU to 100% load, the CPU temperature sensor displays 99°C, probably the X3100 doesn't feel any better.
An observation supporting number 2 is that the problems actually get worse over time, at least that's what I perceive.
So, by now, I think that it is indeed a hardware issue and we all have to throw away our MacBooks sooner or later, but I'd be pleased to see everything fixed by a simple graphics driver update.